HEADER TRANSFERASE 30-APR-10 2KXE TITLE N-TERMINAL DOMAIN OF THE DP1 SUBUNIT OF AN ARCHAEAL D-FAMILY DNA TITLE 2 POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE II SMALL SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-72; COMPND 5 SYNONYM: DP1 SUBUNIT, POL II; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS DNA POLYMERASE, D-FAMILY, SMALL SUBUNIT, ARCHARA, HELICAL BUNDLE, KEYWDS 2 TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.YAMASAKI,I.MATSUI REVDAT 3 14-JUN-23 2KXE 1 REMARK REVDAT 2 26-FEB-20 2KXE 1 REMARK SEQADV REVDAT 1 18-AUG-10 2KXE 0 JRNL AUTH K.YAMASAKI,Y.URUSHIBATA,T.YAMASAKI,F.ARISAKA,I.MATSUI JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE ARCHAEAL JRNL TITL 2 D-FAMILY DNA POLYMERASE SMALL SUBUNIT REVEALS EVOLUTIONARY JRNL TITL 3 RELATIONSHIP TO EUKARYOTIC B-FAMILY POLYMERASES JRNL REF FEBS LETT. V. 584 3370 2010 JRNL REFN ISSN 0014-5793 JRNL PMID 20598295 JRNL DOI 10.1016/J.FEBSLET.2010.06.026 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000101692. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318; 298 REMARK 210 PH : 5.5; 5.5 REMARK 210 IONIC STRENGTH : 0.15; 0.15 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7-3.3MM SODIUM PHOSPHATE; 0.7 REMARK 210 -3.3MM [U-99% 15N] SODIUM REMARK 210 PHOSPHATE; 0.7-3.3MM [U-99% 13C; REMARK 210 U-99% 15N] SODIUM PHOSPHATE; 95% REMARK 210 H2O/5% D2O; 3.3MM [U-99% 15N] REMARK 210 SODIUM PHOSPHATE; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HN(CO)CA; 3D HCCH- REMARK 210 COSY; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N TOCSY; 3D 1H- REMARK 210 13C NOESY; 3D HMQC-NOESY-HMQC; REMARK 210 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 VAL A 65 79.79 -65.45 REMARK 500 1 GLN A 69 -63.61 -106.87 REMARK 500 1 GLU A 70 93.85 60.15 REMARK 500 2 GLU A 45 60.11 62.77 REMARK 500 2 GLU A 70 -176.08 -62.57 REMARK 500 3 GLU A 66 35.03 -154.73 REMARK 500 3 LEU A 67 85.96 -172.67 REMARK 500 3 ILE A 71 140.54 62.95 REMARK 500 4 LEU A 67 70.19 -113.85 REMARK 500 4 GLN A 69 -168.31 -172.14 REMARK 500 4 GLU A 70 -44.90 -161.09 REMARK 500 5 LYS A 31 -62.17 -90.72 REMARK 500 5 ILE A 48 94.96 -69.93 REMARK 500 5 ASP A 50 -168.62 -101.26 REMARK 500 5 ALA A 63 70.92 -104.19 REMARK 500 5 VAL A 65 89.81 64.24 REMARK 500 6 ILE A 15 117.16 -175.58 REMARK 500 6 PHE A 47 31.74 -98.64 REMARK 500 6 LEU A 67 84.88 59.87 REMARK 500 6 GLU A 70 -39.66 -177.35 REMARK 500 7 ASN A 11 30.14 -98.81 REMARK 500 7 PHE A 47 30.70 -98.51 REMARK 500 7 GLN A 69 174.61 -59.34 REMARK 500 8 ASP A 2 74.89 54.87 REMARK 500 8 PHE A 47 43.90 -104.91 REMARK 500 8 GLU A 64 110.95 -170.09 REMARK 500 9 PHE A 47 32.54 -98.62 REMARK 500 9 GLN A 69 -65.00 -147.88 REMARK 500 10 VAL A 65 112.17 -178.02 REMARK 500 10 GLU A 66 -39.69 -178.49 REMARK 500 11 GLU A 66 111.79 62.94 REMARK 500 11 PRO A 68 81.18 -69.51 REMARK 500 11 GLN A 69 94.55 -176.33 REMARK 500 11 GLU A 70 153.90 61.57 REMARK 500 12 THR A 46 109.84 -162.24 REMARK 500 12 GLU A 64 84.53 60.41 REMARK 500 12 LEU A 67 85.66 -155.27 REMARK 500 12 GLU A 70 -177.67 60.22 REMARK 500 13 GLU A 45 62.14 62.74 REMARK 500 13 GLU A 64 95.41 -174.36 REMARK 500 13 ILE A 71 136.64 64.00 REMARK 500 14 PHE A 47 31.12 -98.06 REMARK 500 14 ASP A 50 -169.65 -118.38 REMARK 500 14 VAL A 65 31.03 -98.41 REMARK 500 14 GLU A 66 121.10 -170.06 REMARK 500 14 ILE A 71 150.34 63.60 REMARK 500 15 ASP A 2 62.84 60.29 REMARK 500 15 ILE A 49 93.26 -69.90 REMARK 500 15 ALA A 63 63.61 -106.72 REMARK 500 15 GLU A 66 52.75 -108.87 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16986 RELATED DB: BMRB DBREF 2KXE A 1 72 UNP O57863 DP2S_PYRHO 1 72 SEQADV 2KXE GLY A -2 UNP O57863 EXPRESSION TAG SEQADV 2KXE SER A -1 UNP O57863 EXPRESSION TAG SEQADV 2KXE HIS A 0 UNP O57863 EXPRESSION TAG SEQRES 1 A 75 GLY SER HIS MET ASP GLU PHE VAL LYS GLY LEU MET LYS SEQRES 2 A 75 ASN GLY TYR LEU ILE THR PRO SER ALA TYR TYR LEU LEU SEQRES 3 A 75 VAL GLY HIS PHE ASN GLU GLY LYS PHE SER LEU ILE GLU SEQRES 4 A 75 LEU ILE LYS PHE ALA LYS SER ARG GLU THR PHE ILE ILE SEQRES 5 A 75 ASP ASP GLU ILE ALA ASN GLU PHE LEU LYS SER ILE GLY SEQRES 6 A 75 ALA GLU VAL GLU LEU PRO GLN GLU ILE LYS HELIX 1 1 ASP A 2 LYS A 10 1 9 HELIX 2 2 THR A 16 GLU A 29 1 14 HELIX 3 3 SER A 33 GLU A 45 1 13 HELIX 4 4 ASP A 50 GLY A 62 1 13 SHEET 1 A 2 LEU A 14 ILE A 15 0 SHEET 2 A 2 ILE A 48 ILE A 49 1 O ILE A 49 N LEU A 14 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1